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To mitigate the risk, effluent systems are designed at dairies to reduce run-off.

But there are concerns the effluent management systems in WA are not up to scratch.

The State Government has been offering grants of up to $60,000 for farmers to upgrade their systems to "best practice" through the Regional Estuaries Initiative and the Revitalising Geographe Waterways project.

But in the two and a half years they have been running, just two people have completed upgrades.

Effluent run-off is thought to contribute to algal blooms in waterways.

Every day, tens-of-thousands of litres of effluent is hosed down from the yards into a pond system.

ABC Rural: Tyne Logan

But he said due to the current state of the industry there was no way he could afford the best practice upgrades that the State Government was supporting.

"You're getting $60,000 for a $300,000-$400,000 capital spend and farmers just don't have the capital to commit to the project," he said.

"The incentive isn't large enough relative to the total capital cost, and where dairying is at the moment, there isn't a lot of confidence and therefore people are reluctant to invest.

"I think everyone is conscious of the issue and farmers are doing a lot — fencing waterways, planting trees and distributing fertiliser in responsible ways — but that sort of capital cost is [unaffordable]."

Costs for upgrades vary depending on the size of the farm and the condition of the current system.

What can be done to encourage upgrades?

Mr Woodhouse said a rethink of the incentive program was needed.

"Let's find some middle ground, somewhere where the systems are affordable," he said.

He suggested a slurry system, like the one he has implemented at his property, which sprays the effluent onto dry areas of land to avoid run-off as a more affordable alternative.

High hopes for incentive projects

Ross Woodhouse believes a slurry system might be a cheaper alternative in stopping run-off

Ross Woodhouse believes a slurry system might be a cheaper alternative in stopping run-off

ABC Rural: Tyne Logan

According to the Department of Water and Environmental Regulation, the systems they design are based on the dairy industry's code of practice in WA.

Despite the low uptake so far, the State Government believes the programs will still meet its target of 30 farms by 2020.

Kath Lynch from the Department of Water and Environmental Regulation is heavily involved in both projects and said there were a further 29 people that had put up their hand to be involved in the project.

While these are only expressions of interest, and did not guarantee upgrades will go through, she said she was confident the projects would be a success.

"I think it's an amazingly good uptake, to be honest," Dr Lynch said.

"It's a challenging project and one of the main challenges is the price of milk. If that was better then we would have more uptake, I think."

Dr Lynch said the code of practice on effluent systems was always open to change with further research, but the State Government could not support effluent systems that were not considered best practice.

"Our commitment to the taxpayer who is funding the incentive [the code of practice] is the minimum standard that we will go to," she said.

The power of poo

In the interim, residents of the Shire of Augusta-Margaret River have another solution brewing — turn the poo into power.

Dairy farmers and the Lower Blackwood Land Conservation District Committee have teamed up with Augusta-Margaret River Clean Community Energy to explore the possibility of building a biodigestor at Scott River.

A biodigestor can turn organic matter into energy and also produces a smell-free manure.

Ian Williams from the Augusta-Margaret River Clean Community Energy Group is looking into setting up a biodigestor in Scott River.